Plant Circular RNA Database

Detail information of Zm00001d046579_circ_g.11

			
						 General Information
					
						CircRNA Name
						Zm00001d046579_circ_g.11
					
						ID in PlantcircBase
						zma_circ_009990
					
						Alias
						zma_circ_0003265
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 96793885-96800706  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d046579						
					
						Parent gene annotation
						
							Transcription initiation factor TFIID subunit 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d046579_circ_g.1 Zm00001d046579_circ_g.2 Zm00001d046579_circ_g.3 Zm00001d046579_circ_g.4 Zm00001d046579_circ_g.5 Zm00001d046579_circ_g.6 Zm00001d046579_circ_g.7 Zm00001d046579_circ_g.8 Zm00001d046579_circ_g.9 Zm00001d046579_circ_g.10 Zm00001d046579_circ_g.12 Zm00001d046579_circ_g.13 Zm00001d046579_circ_g.14 						
					
						Support reads
						NA
					
						Tissues
						leaf, root
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							GT-AG							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Zm00001d046579_T001:6
Zm00001d046579_T011:6
Zm00001d046579_T019:6
Zm00001d046579_T018:6
Zm00001d046579_T009:5
Zm00001d046579_T003:6
Zm00001d046579_T007:6
Zm00001d046579_T015:6
Zm00001d046579_T029:6
Zm00001d046579_T005:6
Zm00001d046579_T002:6
Zm00001d046579_T025:6
Zm00001d046579_T006:6
Zm00001d046579_T004:6
Zm00001d046579_T027:6
Zm00001d046579_T031:6
Zm00001d046579_T020:6
Zm00001d046579_T030:6
Zm00001d046579_T016:6
Zm00001d046579_T023:6
Zm00001d046579_T008:6
Zm00001d046579_T024:6

General Information
CircRNA Name	Zm00001d046579_circ_g.11
ID in PlantcircBase	zma_circ_009990
Alias	zma_circ_0003265
Organism	Zea mays
Position	chr9: 96793885-96800706 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d046579
Parent gene annotation	Transcription initiation factor TFIID subunit 1
Parent gene strand	+
Alternative splicing	Zm00001d046579_circ_g.1 Zm00001d046579_circ_g.2 Zm00001d046579_circ_g.3 Zm00001d046579_circ_g.4 Zm00001d046579_circ_g.5 Zm00001d046579_circ_g.6 Zm00001d046579_circ_g.7 Zm00001d046579_circ_g.8 Zm00001d046579_circ_g.9 Zm00001d046579_circ_g.10 Zm00001d046579_circ_g.12 Zm00001d046579_circ_g.13 Zm00001d046579_circ_g.14
Support reads	NA
Tissues	leaf, root
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	GT-AG The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Zm00001d046579_T001:6 Zm00001d046579_T011:6 Zm00001d046579_T019:6 Zm00001d046579_T018:6 Zm00001d046579_T009:5 Zm00001d046579_T003:6 Zm00001d046579_T007:6 Zm00001d046579_T015:6 Zm00001d046579_T029:6 Zm00001d046579_T005:6 Zm00001d046579_T002:6 Zm00001d046579_T025:6 Zm00001d046579_T006:6 Zm00001d046579_T004:6 Zm00001d046579_T027:6 Zm00001d046579_T031:6 Zm00001d046579_T020:6 Zm00001d046579_T030:6 Zm00001d046579_T016:6 Zm00001d046579_T023:6 Zm00001d046579_T008:6 Zm00001d046579_T024:6

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							CAATTCAGTGCTCAAGAAGAAGTCAGCTGCTGCAAAGGGTACCACTGTAACTGGCACTGATGCT
GATCTCCGCAGATTGAGCATGGATGCAGCCCGTGAGctttttgcagaattgaagccttctgaga
agatcaaattgttctgttctgggaaagagcttcaggatgacatctcgttagcaatgcaaaatgt
gcgaccaa

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 1296
Transcript exons: 96793885-96794132,96795073-96795409,96796179-96796385,96
796489-96796581,96797421-96797627,96800503-96800706
CTTTTTGCAGAATTGAAGCCTTCTGAGAAGATCAAATTGTTCTGTTCTGGGAAAGAGCTTCAGG
ATGACATCTCGTTAGCAATGCAAAATGTGCGACCAAACTCCATTGTGCATGCTGTTCGCACTGA
AGTGTACCTATGGCCAAAAGCACAGAAATTACCTGGTGAGGACAAGCCTCTACGCCCTCCTGGG
GCTTTCAGGAAAAAAACTGACTTGTCTATCAAGGATGGACATGTTTTTTTAATGGAATATTGTG
AAGAGAGACCTTTGCTTCTCTCGAATGCAGGAATGGGAGCCCGTCTCTGTACATATTACCAGAA
AACTACCCCTACTGATCAGACAGCTGCATCACTGCGAAACAACAGTGATGGACTGGGCACAGTG
CTTGCAATTGATCCTGCTGATAAATCCCCTTTTCTAGGAGAGATACATTCTGGGTCCCACCAAT
CTTGTCTTGAAACAAACATGTATAGATCACCTGTATTTCCCCATAAGGTTGCACCAACTGATTA
CTTATTAGTTCGTTCAGCCAAAGGGGCTCTTTCCCTCCGTCGCATTGACAAGCTATATGTTGTT
GGCCAACAAGAACCTCATATGGAAGTCTTTTCACCAGGGACTAAGAACATGCAAAATTATCTTC
TGAACCGAGTTCTTGCATATGTTTATCGTGAGTTTCGTGCTAGAGAGAGGCCTGATGCTATTCC
TCAGATTCGAGCTGACGAGTTACCCATACAAAGTCCTCTGACAGAAGCCATAGTGAAAAAACGA
TTGAAGCATTGTGCAGATTTGAAGAAAGGACCAAAGGGGCATTTTTTCTGGACACAGAGACCTG
ATTTCCGGGTTCCATCAGAAGAAGAACTGAGGAGATTATTGACGCCAGAAAGTGTTTGCTGTTA
TGAAAGTATGCAAGCTGGTTTGTATCGTCTCAAGCGCTTAGGAATTCTGAAGCTTACTCAGCCT
GTTGGATTGGCTTCTGCCATGAATCAGCTTCCTGATGAGGCTATTGAGCTTGCTGCTGCATCAC
ATATCGAGAGGGAACTGCAAATCACTAGCTGGAATCTTACAAGTAATTTCGTCGCTTGTACTAA
TCAGGACAGAGAAAATATAGAAAGATTAGAAATCACTGGTGTTGGAGATCCATCTGGTCGTGGG
TTAGGATTCAGCTATGTGCGAGTAGCACCAAAAGCACCTGCCTCCAATTCAGTGCTCAAGAAGA
AGTCAGCTGCTGCAAAGGGTACCACTGTAACTGGCACTGATGCTGATCTCCGCAGATTGAGCAT
GGATGCAGCCCGTGAG
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	CAATTCAGTGCTCAAGAAGAAGTCAGCTGCTGCAAAGGGTACCACTGTAACTGGCACTGATGCT GATCTCCGCAGATTGAGCATGGATGCAGCCCGTGAGctttttgcagaattgaagccttctgaga agatcaaattgttctgttctgggaaagagcttcaggatgacatctcgttagcaatgcaaaatgt gcgaccaa
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 1296 Transcript exons: 96793885-96794132,96795073-96795409,96796179-96796385,96 796489-96796581,96797421-96797627,96800503-96800706 CTTTTTGCAGAATTGAAGCCTTCTGAGAAGATCAAATTGTTCTGTTCTGGGAAAGAGCTTCAGG ATGACATCTCGTTAGCAATGCAAAATGTGCGACCAAACTCCATTGTGCATGCTGTTCGCACTGA AGTGTACCTATGGCCAAAAGCACAGAAATTACCTGGTGAGGACAAGCCTCTACGCCCTCCTGGG GCTTTCAGGAAAAAAACTGACTTGTCTATCAAGGATGGACATGTTTTTTTAATGGAATATTGTG AAGAGAGACCTTTGCTTCTCTCGAATGCAGGAATGGGAGCCCGTCTCTGTACATATTACCAGAA AACTACCCCTACTGATCAGACAGCTGCATCACTGCGAAACAACAGTGATGGACTGGGCACAGTG CTTGCAATTGATCCTGCTGATAAATCCCCTTTTCTAGGAGAGATACATTCTGGGTCCCACCAAT CTTGTCTTGAAACAAACATGTATAGATCACCTGTATTTCCCCATAAGGTTGCACCAACTGATTA CTTATTAGTTCGTTCAGCCAAAGGGGCTCTTTCCCTCCGTCGCATTGACAAGCTATATGTTGTT GGCCAACAAGAACCTCATATGGAAGTCTTTTCACCAGGGACTAAGAACATGCAAAATTATCTTC TGAACCGAGTTCTTGCATATGTTTATCGTGAGTTTCGTGCTAGAGAGAGGCCTGATGCTATTCC TCAGATTCGAGCTGACGAGTTACCCATACAAAGTCCTCTGACAGAAGCCATAGTGAAAAAACGA TTGAAGCATTGTGCAGATTTGAAGAAAGGACCAAAGGGGCATTTTTTCTGGACACAGAGACCTG ATTTCCGGGTTCCATCAGAAGAAGAACTGAGGAGATTATTGACGCCAGAAAGTGTTTGCTGTTA TGAAAGTATGCAAGCTGGTTTGTATCGTCTCAAGCGCTTAGGAATTCTGAAGCTTACTCAGCCT GTTGGATTGGCTTCTGCCATGAATCAGCTTCCTGATGAGGCTATTGAGCTTGCTGCTGCATCAC ATATCGAGAGGGAACTGCAAATCACTAGCTGGAATCTTACAAGTAATTTCGTCGCTTGTACTAA TCAGGACAGAGAAAATATAGAAAGATTAGAAATCACTGGTGTTGGAGATCCATCTGGTCGTGGG TTAGGATTCAGCTATGTGCGAGTAGCACCAAAAGCACCTGCCTCCAATTCAGTGCTCAAGAAGA AGTCAGCTGCTGCAAAGGGTACCACTGTAACTGGCACTGATGCTGATCTCCGCAGATTGAGCAT GGATGCAGCCCGTGAG
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.133551634

Conservation Information
Conserved circRNAs	NA
PMCS	0.133551634

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							96793967-96800703(+)
						
					

						Potential amino acid sequence
						
							MQNVRPNSIVHAVRTEVYLWPKAQKLPGEDKPLRPPGAFRKKTDLSIKDGHVFLMEYCEERPLL
LSNAGMGARLCTYYQKTTPTDQTAASLRNNSDGLGTVLAIDPADKSPFLGEIHSGSHQSCLETN
MYRSPVFPHKVAPTDYLLVRSAKGALSLRRIDKLYVVGQQEPHMEVFSPGTKNMQNYLLNRVLA
YVYREFRARERPDAIPQIRADELPIQSPLTEAIVKKRLKHCADLKKGPKGHFFWTQRPDFRVPS
EEELRRLLTPESVCCYESMQAGLYRLKRLGILKLTQPVGLASAMNQLPDEAIELAAASHIEREL
QITSWNLTSNFVACTNQDRENIERLEITGVGDPSGRGLGFSYVRVAPKAPASNSVLKKKSAAAK
GTTVTGTDADLRRLSMDAARELFAELKPSEKIKLFCSGKELQDDISLAMQNVRPNSIVHAVRTE
VYLWPKAQKLPGEDKPLRPPGAFRKKTDLSIKDGHVFLMEYCEERPLLLSNAGMGARLCTYYQK
TTPTDQTAASLRNNSDGLGTVLAIDPADKSPFLGEIHSGSHQSCLETNMYRSPVFPHKVAPTDY
LLVRSAKGALSLRRIDKLYVVGQQEPHMEVFSPGTKNMQNYLLNRVLAYVYREFRARERPDAIP
QIRADELPIQSPLTEAIVKKRLKHCADLKKGPKGHFFWTQRPDFRVPSEEELRRLLTPESVCCY
ESMQAGLYRLKRLGILKLTQPVGLASAMNQLPDEAIELAAASHIERELQITSWNLTSNFVACTN
QDRENIERLEITGVGDPSGRGLGFSYVRVAPKAPASNSVLKKKSAAAKGTTVTGTDADLRRLSM
DAARELFAELKPSEKIKLFCSGKELQDDISLAMQNVRPNSIVHAVRTEVYLWPKAQKLPGEDKP
LRPPGAFRKKTDLSIKDGHVFLMEYCEERPLLLSNAGMGARLCTYYQKTTPTDQTAASLRNNSD
GLGTVLAIDPADKSPFLGEIHSGSHQSCLETNMYRSPVFPHKVAPTDYLLVRSAKGALSLRRID
KLYVVGQQEPHMEVFSPGTKNMQNYLLNRVLAYVYREFRARERPDAIPQIRADELPIQSPLTEA
IVKKRLKHCADLKKGPKGHFFWTQRPDFRVPSEEELRRLLTPESVCCYESMQAGLYRLKRLGIL
KLTQPVGLASAMNQLPDEAIELAAASHIERELQITSWNLTSNFVACTNQDRENIERLEITGVGD
PSGRGLGFSYVRVAPKAPASNSVLKKKSAAAKGTTVTGTDADLRRLSMDAARELFAELKPSEKI
KLFCSGKELQDDISLAMQNVRPNSIVHAVRTEVYLWPKAQKLPGEDKPLRPPGAFRKKTDLSIK
DGHVFLMEYCEERPLLLSNAGMGARLCTYYQKTTPTDQTAASLRNNSDGLGTVLAIDPADKSPF
LGEIHSGSHQSCLETNMYRSPVFPHKVAPTDYLLVRSAKGALSLRRIDKLYVVGQQEPHMEVFS
PGTKNMQNYLLNRVLAYVYREFRARERPDAIPQIRADELPIQSPLTEAIVKKRLKHCADLKKGP
KGHFFWTQRPDFRVPSEEELRRLLTPESVCCYESMQAGLYRLKRLGILKLTQPVGLASAMNQLP
DEAIELAAASHIERELQITSWNLTSNFVACTNQDRENIERLEITGVGDPSGRGLGFSYVRVAPK
APASNSVLKKKSAAAKGTTVTGTDADLRRLSMDAARE(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	96793967-96800703(+)
Potential amino acid sequence	MQNVRPNSIVHAVRTEVYLWPKAQKLPGEDKPLRPPGAFRKKTDLSIKDGHVFLMEYCEERPLL LSNAGMGARLCTYYQKTTPTDQTAASLRNNSDGLGTVLAIDPADKSPFLGEIHSGSHQSCLETN MYRSPVFPHKVAPTDYLLVRSAKGALSLRRIDKLYVVGQQEPHMEVFSPGTKNMQNYLLNRVLA YVYREFRARERPDAIPQIRADELPIQSPLTEAIVKKRLKHCADLKKGPKGHFFWTQRPDFRVPS EEELRRLLTPESVCCYESMQAGLYRLKRLGILKLTQPVGLASAMNQLPDEAIELAAASHIEREL QITSWNLTSNFVACTNQDRENIERLEITGVGDPSGRGLGFSYVRVAPKAPASNSVLKKKSAAAK GTTVTGTDADLRRLSMDAARELFAELKPSEKIKLFCSGKELQDDISLAMQNVRPNSIVHAVRTE VYLWPKAQKLPGEDKPLRPPGAFRKKTDLSIKDGHVFLMEYCEERPLLLSNAGMGARLCTYYQK TTPTDQTAASLRNNSDGLGTVLAIDPADKSPFLGEIHSGSHQSCLETNMYRSPVFPHKVAPTDY LLVRSAKGALSLRRIDKLYVVGQQEPHMEVFSPGTKNMQNYLLNRVLAYVYREFRARERPDAIP QIRADELPIQSPLTEAIVKKRLKHCADLKKGPKGHFFWTQRPDFRVPSEEELRRLLTPESVCCY ESMQAGLYRLKRLGILKLTQPVGLASAMNQLPDEAIELAAASHIERELQITSWNLTSNFVACTN QDRENIERLEITGVGDPSGRGLGFSYVRVAPKAPASNSVLKKKSAAAKGTTVTGTDADLRRLSM DAARELFAELKPSEKIKLFCSGKELQDDISLAMQNVRPNSIVHAVRTEVYLWPKAQKLPGEDKP LRPPGAFRKKTDLSIKDGHVFLMEYCEERPLLLSNAGMGARLCTYYQKTTPTDQTAASLRNNSD GLGTVLAIDPADKSPFLGEIHSGSHQSCLETNMYRSPVFPHKVAPTDYLLVRSAKGALSLRRID KLYVVGQQEPHMEVFSPGTKNMQNYLLNRVLAYVYREFRARERPDAIPQIRADELPIQSPLTEA IVKKRLKHCADLKKGPKGHFFWTQRPDFRVPSEEELRRLLTPESVCCYESMQAGLYRLKRLGIL KLTQPVGLASAMNQLPDEAIELAAASHIERELQITSWNLTSNFVACTNQDRENIERLEITGVGD PSGRGLGFSYVRVAPKAPASNSVLKKKSAAAKGTTVTGTDADLRRLSMDAARELFAELKPSEKI KLFCSGKELQDDISLAMQNVRPNSIVHAVRTEVYLWPKAQKLPGEDKPLRPPGAFRKKTDLSIK DGHVFLMEYCEERPLLLSNAGMGARLCTYYQKTTPTDQTAASLRNNSDGLGTVLAIDPADKSPF LGEIHSGSHQSCLETNMYRSPVFPHKVAPTDYLLVRSAKGALSLRRIDKLYVVGQQEPHMEVFS PGTKNMQNYLLNRVLAYVYREFRARERPDAIPQIRADELPIQSPLTEAIVKKRLKHCADLKKGP KGHFFWTQRPDFRVPSEEELRRLLTPESVCCYESMQAGLYRLKRLGILKLTQPVGLASAMNQLP DEAIELAAASHIERELQITSWNLTSNFVACTNQDRENIERLEITGVGDPSGRGLGFSYVRVAPK APASNSVLKKKSAAAKGTTVTGTDADLRRLSMDAARE(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d046579_circ_g.11

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